I too don't think that the Supes in S/B is the Kingdom Commer.
For one thing, he's a lot more bitter. He just doesn't seem to be the same guy. I think it's just a Superman from the future who uses that shield.
As for other weird things, I mean, freakin' in Superman/Batman, Lex has just set a billion dollar bounty on the S-man.
Will all this evidence we have... something will be going down... I'm betting it will be after Azz and Lee's 12 issue Superman run, and then Lee and Loeb returned for six Batman issues. That will free him up to pencil Hypercrisis or whatever it is. Either him... or they get Perez for one final hurrah...